You can specify their origin with the property protons:generatedBy. This way you mark every instance from DBpedia as being generated by http://dbpedia.org/page/DBpedia.
There are various approaches to retrieve the complete list of entities. In this case you can use regular expressions and bash to extract them from dbpedia_instances.nt file.
Create the RDF and store it in a file called dbpedia_generated_by.n3 . Put the file in the dbpedia folder, and then add (kb/dbpedia/dbpedia_generated_by.n3) to the list of imports and defaultNS definitions in KIM/config/owlim.ttl.